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17 protocols using dfc400

1

Placental Trophoblast Outgrowth and PD-L1 Silencing

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Briefly, villous explants with potential EVT columns were carefully dissected and positioned on 24-well plates (Corning) precoated with 200 μL of Matrigel (BD Biocoat, 356234), which was diluted 1:1 with DMEM/F12 medium. After 24 h of culture, villous tips were examined under a dissecting microscope for successful EVT outgrowth. All successful explants were selected for treatment with 250 nM of oligomers (siCtrl or siPD-L1 group). Explants were photographed immediately after adding the treatment and subsequently at 48 h using a Leica DFC400 camera attached to a dissecting microscope. ImageJ was used to measure the distance of EVT outgrowth. Specifically, the total outgrowth area was calculated by subtracting the distance at the end point from the initial area upon treatment. Each experiment was designed with a minimum of four replicates and was repeated on three different placentas. Then, the expression of HLA-G (Abcam), a marker protein of EVT, was detected by immunofluorescence staining. Additionally, the fluorescent microscope (Leica DFC400) was used to demonstrate the efficient knockdown of PD-L1.
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2

Taxonomic Identification of Cumacean Specimens

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A total of 947 specimens (Table S2) were determined to the lowest possible taxonomic rank, based primarily on original species descriptions (e.g., Hansen, 1920 (link); Sars, 1900 ). Species identifications were conducted at the Department of Biological Sciences (University of Bergen, Norway) and DZMB Hamburg using either a ZEISS SteREO Discovery V8 or Leica MZ12.5 dissecting microscope. Dissected pereopods and mouth parts were assessed under a ZEISS Primo Star compound microscope. High quality pictures with depth of focus were taken with a Leica DFC400 digital compound microscope camera using the Z-stacking option in the Leica Application Suite imaging software. Current authoritative classification follows the catalogue World Cumacea Database (http://www.marinespecies.org/cumacea/, Watling & Gerken, 2019 ) in the World Register of Marine Species (WoRMS Editorial Board, 2019 ). Additionally, comparative museums’ material has been obtained from the Center of Natural History Hamburg (CeNak) and the University Museum of Bergen (ZMBN).
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3

Trophoblast Outgrowth Assay Protocol

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Explant cultures were performed as previously described (34 (link), 40 (link)). Briefly, villous explants with potential EVT columns were carefully dissected and positioned on Transwell inserts (Millipore, Billerica, MA) pre-coated with 200 μL of undiluted phenol red-free Matrigel (BD Biosciences, Bedford, MA). Explants were left overnight to attach to the Matrigel, at 37°C with 3% O2 and 5% CO2, before adding serum-free DMEM-F12 medium supplemented with 100 U/mL of penicillin, 100 U/mL of streptomycin, 100 μg/mL Normacin™. After 2 days of culture, villous tips were examined under the dissecting microscope for successful EVT outgrowths. All successful explants were selected for treatment with 200 nM oligomers (Table 3). Explants were photographed immediately after adding treatment, and subsequently at 48 h, using a Leica DFC400 camera attached to a dissecting microscope. ImageJ was used to measure the area of EVT outgrowth. Specifically, total outgrowth area was calculated by subtracting the area at the end point with the initial area upon treatment. Each experiment was designed with a minimum of four replicates, and was repeated on three different placentas.
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4

Rhodamine123 Uptake in Tick Organs

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To investigate the route of water intake in ticks, 1.28 µL of 1 mM rhodamine123 in water (Sigma-Aldrich, St. Louis, MO, USA) was filled in a microcapillary tube (Diameter ∼0.11 mm, Sigma-Aldrich, St. Louis, MO, USA) and the tube was placed onto the mouthparts of dehydrated unfed female ticks. Ticks were allowed to ingest Rh123 under rehydration conditions (RH 98%) at room temperature for 30 min. After ingestion, we quantified the ingested amount and traced the locations of fluorescence signal in tick organs, specifically in the salivary glands and the gut diverticular. The volume ingested was calculated by the equation for cylinder volume (V = πr2h). For calculation of volume, the reduced length (h) of fluid in microcapillary tubes was measured under a grid microscope and analyzed with r2 = 0.0127. The locations of fluorescence in the internal organs were identified after dorsal integument of ticks was removed by a surgical scalpel. Images were captured using a camera (DFC400) attached to a stereo microscope (M205FA; Leica, Heerbrugg, Switzerland). Salivary glands were subsequently dissected out, fixed in 4% paraformaldehyde at room temperature for 30 min, washed in PBST (0.1% Triton X-100), and imaged on a confocal microscope (LSM700; Zeiss, Oberkochen, Germany).
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5

In Situ Hybridization of gdf6a and gdf6b

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RNA sense and anti-sense probes were synthesized from pcsDest2-gdf6a and pcsDest2-gdf6b constructs using DIG RNA Labeling Kit (Roche) per the manufacturer’s instruction. Wild-type embryos of the appropriate stage were fixed in 4% PFA at 4°C for 24 hr. Following fixation, embryos were dehydrated in methanol at stored at −20°C. Whole mount in situ hybridization was performed as previously described (Reichert et al., 2013 (link)). Hybridized probes were detected using anti-digoxigenin (DIG) antibodies tagged with alkaline-phosphatase (AP) (Roche) using NBT/BCIP (Roche) solution per the manufacturer’s instructions. Stained embryos were mounted in 2.5% methylcellulose and imaged using a Leica M165FC microscope and Leica DFC400 camera. Specificity of the probes was verified using sense probes synthesized from the same construct.
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6

Fluoride Water Treatment Effects on Rodent Teeth

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After fluoride water treatment with control-chow or 4PBA-chow for 6 weeks, animals were euthanized. Heads were cleaned of fur and skin. Photographs of the maxillary and mandibular incisors were taken using a Nikon SMZ745T microscope and Leica DFC400 digital camera under standard white balance and lighting conditions.
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7

Microscopic Imaging Acquisition and Processing

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Images were acquired with an inverted microscope (Leica-DMI6000B) equipped with Leica DFC365FX and DFC400 cameras and ×10 and ×20 magnification objectives. The Leica Application Suite software was used for acquisition, while Photoshop was used to generate merged images.
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8

Quantifying Muscle Damage and Regeneration

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Images were acquired with an inverted microscope (Leica-DMI6000B) equipped with Leica DFC365FX and DFC400 cameras and 20× and 40× magnification objectives. Necrotic myofibers were defined as pink pale patchy fibers, and phagocyted myofibers were defined as pink pale fibers invaded by basophilic single cells (MPs). For the quantification of CSA, analyses were done on damaged TA, which presented at least 75% of injured muscle. At least 8 pictures in different fields were taken and at least 500 myofibers were analyzed. For each condition of each experiment, at least 8 fields chosen randomly were counted. The number of labelled MPs or mpcs was calculated using the cell tracker in ImageJ software and expressed as a percentage of total MPs or mpcs. Fusion index was the number of nuclei within myotubes divided by the total number of nuclei.
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9

Quantifying Melanocyte Regeneration in Zebrafish

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Whole-fish images were captured using a Nikon D90 camera equipped with SB-R200 wireless remote speedlights. Fish with fluorescent markers were viewed with a Leica M165FC stereomicroscope or a Leica DM550B compound microscope and images captured with Leica DFC400 or DFC365FX cameras, respectively. Brightfield images were adjusted for contrast and color balance for clarity. Sections were viewed with a Leica DM550B compound microscope and images were captured with DFC365FX or DMC2900 cameras. To quantify the effect of IWR-1 on melanocyte regeneration, flanks of fish were imaged and melanocytes counted on the left side center stripe of each fish in a rectangular region delimited as a 5.8mm×1.2mm window with its left boundary 1mm posterior to the edge of the operculum. Percent regeneration was calculated as a ratio of the number of melanocytes within the region at the specified time point to the number of melanocytes within the region prior to neocuproine treatment. Student’s t-tests were performed using Prism 6.
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10

Quantifying Skeletal Muscle Morphology

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Images of stained muscle slices were acquired by nanozoomer S60 (Hamamatsu) of Unitech NoLimits facility at University of Milan. Images of IF were acquired by the inverted microscope (Leica-DMI6000B) equipped with Leica DFC365FX and DFC400 cameras and ×10, ×20, ×40 magnification objectives. The Leica Application Suite software was used for acquisition.
The cross-sectional area (CSA) of myofibers was evaluated on anti-Laminin immunofluorescent staining of Tibialis anterior and Diaphragm muscle sections. Images of the entire section were split into two-half and separately analyzed with the Open-CSAM tool of the ImageJ software.67 (link) The ImageJ software was used to calculate the average myotube length in vitro.
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